Loading trajectories
To initialize a trajectory file for computation, use the command
trajectory = Trajectory("trajectory.xtc",solute,solvent)where solute and solvent are defined with the AtomSelection function described before. This function opens the stream for reading frames, which are read once a time when the coordinates are required for computing the MDDF.
The Trajectory function uses Chemfiles in background, and thus the most common trajectory formats are supported, as the ones produced with NAMD, Gromacs, LAMMPS, Amber, etc.
The format of the trajectory file is automatically determined by Chemfiles from the extension of the file. However, it can be provided by the user with the format keyword, for example:
trajectory = Trajectory("trajectory.xtc",solute,solvent,format="xtc")Reference functions
ComplexMixtures.Trajectory — TypeTrajectory(filename::String, solute::AtomSelection, solvent::AtomSelection; format::String = "", chemfiles = false)Trajectory constructor data type.
Defaults to reading with the Chemfiles infrastructure, except for DCD and PDB trajectory files, if the "PDBTraj" option is provided.
See memory issue (https://github.com/chemfiles/Chemfiles.jl/issues/44)